Interresting opinions here. I would like to throw a rock into the bush.....
What if Microsoft made a great Flight Simulator, and they just give you a bunch of files, and tells you via Readme file how to install, and where each file and folder should go? I think one of the reasons people use auto installers, is to be professional.
I was going to leave it there but I don't think that's a good example. I would expect a professional outfit like Microsoft to get things right. Otherwise they wouldn't stay in business long. Mind you, FSX was not the best example of professionalism. IMHO
The point here is that we're talking about Freeware which is created by amateurs who do not necessarily know what they're doing. Anyone can create addons for MSFS/CFS & post them on a website for others to download with absolutely no guarantee or support. Some Freeware developers might be very good at what they do but that doesn't mean that they know the best way to install their own files. Consequently they won't know how to configure an auto-installer.
Over the years I've seen many downloads created by experienced Freeware developers that would have completely messed up FS if they had been installed as directed in the author's Readme instructions. This proves that the addon was never tested properly before being unleashed on an unsuspecting public. Possibly the worst advice commonly seen in these instructions is to unzip files direct to the sim. This is exactly the same as what an auto-installer does & if there is some fault with the configuration or it's not directed to the correct location it will never work properly & you might never find where on your PC those files went.
Another common mistake is including default files that the end-user should already have installed. If these are corrupt or older than the originals they will overwrite the default files which will possibly cause problems. I could go on but hope I've made my point.

if you don't trust the auto installer, because of a previous mishap, feel free to direct to a temp folder and install manually. This is a option I wrote into my auto installer, so the end user can use either the auto installer, or do it manually.
That's exactly what I did with the Fox Four campaigns for CFS2 that I configured some years ago. The files are configured as self-extracting zipfiles which can be manually extracted just like conventional zipfiles with the usual right-click option if preferred. This is pointed out in the Readme & also on the download & Help pages of the Fox Four website. Campaigns can be difficult to install & we attempted to make the project as professional & user-friendly as possible and also support it indefinitely. Several years later I think we succeeded & we've had very few reported problems, mainly from people who didn't bother reading the simple instructions. One thing we agreed on before uploading anything was that we would never deliberately modify or overwrite default files. I think this is the right approach & nobody will convince me otherwise.

PS. You have to bear in mind that the most likely people to use auto-installers are beginners to the hobby or those who never figured out how to do it manually. These are the very people who will have problems if the files are faulty in any way.